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Increased detection of circulating tumor DNA by short fragment enrichment

BACKGROUND: Circulating cell-free DNA (cfDNA) detection for non-invasive diagnosis requires higher sensitivity and accuracy due to the low circulating tumor DNA (ctDNA) content. Many methods have been developed to improve detection of ctDNA, including ultra-deep sequencing or enrichment of shorter c...

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Autores principales: Liu, Yang, Liu, Yangyang, Wang, Yingying, Li, Lei, Yao, Wenjun, Song, Yingnan, Liu, Bing, Chen, Weihuang, Santarpia, Mariacarmela, Rossi, Elisabetta, Zamarchi, Rita, Wang, Zhe, Wang, Qiming, Cheng, Gang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: AME Publishing Company 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8044499/
https://www.ncbi.nlm.nih.gov/pubmed/33889525
http://dx.doi.org/10.21037/tlcr-21-180
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author Liu, Yang
Liu, Yangyang
Wang, Yingying
Li, Lei
Yao, Wenjun
Song, Yingnan
Liu, Bing
Chen, Weihuang
Santarpia, Mariacarmela
Rossi, Elisabetta
Zamarchi, Rita
Wang, Zhe
Wang, Qiming
Cheng, Gang
author_facet Liu, Yang
Liu, Yangyang
Wang, Yingying
Li, Lei
Yao, Wenjun
Song, Yingnan
Liu, Bing
Chen, Weihuang
Santarpia, Mariacarmela
Rossi, Elisabetta
Zamarchi, Rita
Wang, Zhe
Wang, Qiming
Cheng, Gang
author_sort Liu, Yang
collection PubMed
description BACKGROUND: Circulating cell-free DNA (cfDNA) detection for non-invasive diagnosis requires higher sensitivity and accuracy due to the low circulating tumor DNA (ctDNA) content. Many methods have been developed to improve detection of ctDNA, including ultra-deep sequencing or enrichment of shorter cfDNA fragments, such as those in the range of 90–150 bp. METHODS: Here, we developed a method for single-stranded DNA (ssDNA) library preparation with a large proportion of magnetic beads to enrich the shorter cfDNA fragments. We aimed to determine if this could increase the ctDNA content and thus improve the sensitivity of ctDNA detection by testing the method in blood samples from patients with advanced cancers (non-small cell lung cancers, esophageal squamous cell carcinoma, cholangiocarcinoma, colorectal cancer and liver cancer). RESULTS: This method was able to obtain shorter cfDNA both in commercial cfDNA references and real world clinical cfDNA samples. Plasmid simulation experiments showed that using a large proportion of magnetic beads to construct the library could obtain more ctDNA derived from shorter-fragment plasmids, which could significantly improve the detection of ctDNA especially in the low-variant allele frequency sample. In real-world clinical samples, this method may be able to increase the opportunity to obtain alteration reads from short fragments, which was important to low frequency detection. CONCLUSIONS: The ssDNA library preparation with large proportion of magnetic beads could increase the opportunity to obtain alteration reads from short fragments, which is crucial for low variant allele frequency detection.
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spelling pubmed-80444992021-04-21 Increased detection of circulating tumor DNA by short fragment enrichment Liu, Yang Liu, Yangyang Wang, Yingying Li, Lei Yao, Wenjun Song, Yingnan Liu, Bing Chen, Weihuang Santarpia, Mariacarmela Rossi, Elisabetta Zamarchi, Rita Wang, Zhe Wang, Qiming Cheng, Gang Transl Lung Cancer Res Original Article BACKGROUND: Circulating cell-free DNA (cfDNA) detection for non-invasive diagnosis requires higher sensitivity and accuracy due to the low circulating tumor DNA (ctDNA) content. Many methods have been developed to improve detection of ctDNA, including ultra-deep sequencing or enrichment of shorter cfDNA fragments, such as those in the range of 90–150 bp. METHODS: Here, we developed a method for single-stranded DNA (ssDNA) library preparation with a large proportion of magnetic beads to enrich the shorter cfDNA fragments. We aimed to determine if this could increase the ctDNA content and thus improve the sensitivity of ctDNA detection by testing the method in blood samples from patients with advanced cancers (non-small cell lung cancers, esophageal squamous cell carcinoma, cholangiocarcinoma, colorectal cancer and liver cancer). RESULTS: This method was able to obtain shorter cfDNA both in commercial cfDNA references and real world clinical cfDNA samples. Plasmid simulation experiments showed that using a large proportion of magnetic beads to construct the library could obtain more ctDNA derived from shorter-fragment plasmids, which could significantly improve the detection of ctDNA especially in the low-variant allele frequency sample. In real-world clinical samples, this method may be able to increase the opportunity to obtain alteration reads from short fragments, which was important to low frequency detection. CONCLUSIONS: The ssDNA library preparation with large proportion of magnetic beads could increase the opportunity to obtain alteration reads from short fragments, which is crucial for low variant allele frequency detection. AME Publishing Company 2021-03 /pmc/articles/PMC8044499/ /pubmed/33889525 http://dx.doi.org/10.21037/tlcr-21-180 Text en 2021 Translational Lung Cancer Research. All rights reserved. https://creativecommons.org/licenses/by-nc-nd/4.0/Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0 (https://creativecommons.org/licenses/by-nc-nd/4.0/) .
spellingShingle Original Article
Liu, Yang
Liu, Yangyang
Wang, Yingying
Li, Lei
Yao, Wenjun
Song, Yingnan
Liu, Bing
Chen, Weihuang
Santarpia, Mariacarmela
Rossi, Elisabetta
Zamarchi, Rita
Wang, Zhe
Wang, Qiming
Cheng, Gang
Increased detection of circulating tumor DNA by short fragment enrichment
title Increased detection of circulating tumor DNA by short fragment enrichment
title_full Increased detection of circulating tumor DNA by short fragment enrichment
title_fullStr Increased detection of circulating tumor DNA by short fragment enrichment
title_full_unstemmed Increased detection of circulating tumor DNA by short fragment enrichment
title_short Increased detection of circulating tumor DNA by short fragment enrichment
title_sort increased detection of circulating tumor dna by short fragment enrichment
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8044499/
https://www.ncbi.nlm.nih.gov/pubmed/33889525
http://dx.doi.org/10.21037/tlcr-21-180
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